Transforms the coordinates of short reads between two species. RECOT is a set of programs that converts the alignment or mapping coordinates of short reads obtained from the query species to a comparison target species. The software allows comparative genomics and comparative transcriptomics between model and non-model organisms. It can be used for species in which the genome sequence is unavailable.
Converts genomic segments among assemblies. segment_liftover is a program able to considerer both probe and segments files of any species. The application includes functionalities permitting to perform a batch processing of multiple files, access to detailed logs and the ability to perform a re-conversion by locus approximation. The software can also be incorporated into data processing pipelines.
Permits to transfer annotation from a source to another. NCBI Genome Remapping Service performs three types of query: (i) assembly-assembly for projecting features from a selected assembly to another; (ii) clinical remap for transferring data from an assembly sequences to RefSeqGene sequences and; (iii) alt loci remap for remapping features from the Primary assembly unit and the Alternate Loci and Patches assembly units.
Converts coordinates on one genome assembly to another. Assembly Converter shows all available mapping events for your chosen species, including conversions from old assemblies to newer ones and conversions back to old from new. Input coordinates in one of the specified formats, and the user will receive a file in the same format with coordinates on the different assembly.
Converts genome coordinates and genome annotation files between assemblies. UCSC LiftOver is a pipeline that can be used to convert coordinate ranges between genome assemblies. It supports forward/reverse conversions, batch conversions, and conversions between species.